It happened to me. I used DPGTools13 from the latest moonshell package to convert some videos. I couldn't watch the videos on my R4 for some reason and I couldn't figure out why. So... I replaced the moonshell files on the R4 with the newer moonshell that I just downloaded (v1.71), and it works!
So in conclusion, videos converted with the new dpgtools, must be played with the new moonshell.
There is one bug though, pressing Start in the new moonshell doesn't bring me back to the R4's main page anymore.